Have you ever played a really old Mac game on a newer Mac? They are sometimes inadvertently programmed in such a way that relies on the speed of the CPU, so they run WAY too fast to even play on the newer Mac. Old versions of Brickles are like that.
It could be that part of the system loads too fast because of the speedy CPU and is expecting something else to have already taken place, maybe some piece of hardware to be initialized. In all circumstances during development, it may not have been possible for the CPU to outrun the offending issue, and now that it can, it just crashes when it happens.
Another possibility is defective hardware. Classic Mac OS utilizes hardware differently than OS X. For example, if you had a sketchy Rage Pro video card, Mac OS X would not use the 3D acceleration of that card and OS 9 would, thus causing crashing only in OS 9. There could be a special function of the CPU, some sort of extra boost that OS X does not support, and similarly when utilized in OS 9, produces the crash.